Tag Archives: dovdox blog

An automatic relay of postings from dovdox.com.

What’s in a (Domain) Name?

Just over three years ago, I deleted my Facebook account and promised my friends (and “friends”) that I’d keep posting the same sorts of updates here, on the flagship vanity domain for my name. Meanwhile, I would put my work-related postings on a separate blog on my old dovdox.com domain, for people who only wanted to read my science blogging.

I failed.

The problem was my old domain name, dovdox.com. I’d originally bought it as a site for both me (Alan Dove, Ph.D.) and my wife (Laura Dove, M.D.). The Dove Docs. Get it? It was a great domain for that imagined purpose, but it turned out that Laura didn’t really have a use for her own site, and besides testing the occasional bit of server software my only real use for it was blogging. Dovdox makes a lot less sense as a science blog title. I eventually redirected incoming dovdox.com traffic here, and this became my only blog.

That didn’t really work either. People who want to read my science writing are interested in science, not what I get up to in my spare time. Friends and family members want more pictures of my kid. I need two separate sites, each designed from the domain up for a specific audience.

So here’s the new arrangement. This site is now my personal page. It’s about me, my rambling thoughts, my family, my friends, and the things we do – at least the parts I feel like publishing. A feed from my new science blog will also provide links to whatever I post there, so this site will have the whole stream of my online output. It’s my version of a Facebook wall. Incidentally, if everyone had a personal blog, we could all just subscribe to each others’ RSS feeds and watch Facebook die. Think about it.

My new science blog is The Turbid Plaque. It’ll be about science, science journalism, and science policy. If you’re here for the science – or you’re just curious about how I arrived at that title – pop on over there.

The “Thank You for Smoking” Effect?

Today’s issue of MMWR includes an interesting analysis of the prevalence of smoking among characters in top-grossing American movies. The statistics span 1991-2009, during which time the authors noticed an apparent trend:

This report summarizes the results of that study, which found that the number of tobacco incidents depicted in the movies during this period peaked in 2005 and then progressively declined. Top-grossing movies released in 2009 contained 49% of the number of onscreen smoking incidents as observed in 2005 (1,935 incidents in 2009 versus 3,967 incidents in 2005). Further reduction of tobacco use depicted in popular movies could lead to less initiation of smoking among adolescents. Effective methods to reduce the potential harmful influence of onscreen tobacco use should be implemented.

The data are pretty noisy, though. For example, while the past four years appear to show a decline, the number of smoking “incidents” in 2009 is still higher than the 1998 level, and there’s tremendous year-to-year variation.

If there really has been a decline in smoking in movies, though, what might have caused it? Is it just coincidence that a fairly successful film satirized exactly this type of product placement in 2005, precisely when the decline began?

We Are Eggsperiencing Delays

As everyone has already heard, there’s been a bit of a problem with the US egg supply. Today, the New York Times and other sources report that it’s getting even worse. Buried in the reporting is a pretty typical food poisoning timeline:

The salmonella outbreak began in May, when several states began seeing an increase in the number of cases of a common type of bacterial illness known as Salmonella enteritidis, said Dr. Christopher R. Braden, acting director of food-borne diseases at the Centers for Disease Control and Prevention in Atlanta. The numbers continued to grow, and in June and July, a database used to track disease nationwide found that the number of cases had risen from a historical average of about 50 a week to about 200.

Public health officials in California, Minnesota and Colorado determined that many of the people who had gotten sick had eaten food containing eggs. Further investigation traced many tainted eggs to Wright County Egg.

Incredible (edible?) eggs.

Incredible (edible?) eggs. Image courtesy woodleywonderworks.

So officials started to suspect a problem in May, were probably pretty sure of it by June or July, and we’re just getting around to recalling these products in late August. Why does it take so long to stop a pathogen that only has a 24 to 72-hour incubation period?

There are a few reasons. Public health departments have accelerated their data-sharing dramatically in recent years, but there’s still room for improvement. It also takes time just to figure out which ingredient is causing a foodborne outbreak, and more time to trace it to its source. The biggest delay, though, may come from the big food processors themselves, who have an enormous motivation to stall such an investigation. As the Times explains:

The company announced on Friday that it was recalling 228 million eggs that it had sold since mid-May. On Wednesday, it added another 152 million eggs to the recall. Many of the affected eggs have long since been cooked and eaten, but millions could still be stored in refrigerators.

You don’t have to refund someone’s money for an egg that’s already been sold, cooked, and eaten. Wait another week, and there won’t be anything left to recall at all.

MRSA-Killing Paint: Very Cool, but Not Cheap

Researchers at Rensselaer Polytechnic Institute have created a new type of paint with a very impressive capability: it kills methicillin-resistant Staphylococcus aureus (MRSA), the bacterium that haunts the nightmares of many microbiologists. Unlike previous MRSA-killing paints, this one doesn’t seem to get clogged with dead bacteria, so it keeps on killing for months. Even better, it uses an antimicrobial agent that is nontoxic to pretty much everything except MRSA:

“We’re building on nature,” said Jonathan S. Dordick, the Howard P. Isermann Professor of Chemical and Biological Engineering, and director of Rensselaer’s Center for Biotechnology & Interdisciplinary Studies. “Here we have a system where the surface contains an enzyme that is safe to handle, doesn’t appear to lead to resistance, doesn’t leach into the environment, and doesn’t clog up with cell debris. The MRSA bacteria come in contact with the surface, and they’re killed.”

In tests, 100 percent of MRSA in solution were killed within 20 minutes of contact with a surface painted with latex paint laced with the coating.

The new coating marries carbon nanotubes with lysostaphin, a naturally occurring enzyme used by non-pathogenic strains of Staph bacteria to defend against Staphylococcus aureus, including MRSA. The resulting nanotube-enzyme “conjugate” can be mixed with any number of surface finishes — in tests, it was mixed with ordinary latex house paint.

Lysostaphin 3-dimensional structure, image courtesy Wikimedia Commons.

Lysostaphin 3-dimensional structure, image courtesy Wikimedia Commons.

The active ingredient is even available off the shelf from at least one supplier. Before you rush out to repaint the local hospital, though, gird your loins for the bill. “Bulk” orders of 4 grams or more of lysostaphin qualify for the discounted price of only $6,800 per gram (nanotubes sold separately). You might want to skip sanding between coats.

Presidential Elections and Suicide Rates

In new work that just might be another proof of the ease of finding bizarre correlations, researchers at Texas A&M University have found that people who voted for the loser in a Presidential election may be less likely to kill themselves than those who voted for the winner. As the lead author explains in an accompanying press release:

In states where the majority of voters supported the national election winner suicide rates decreased. However, counter-intuitively, suicide rates decreased even more dramatically in states where the majority of voters supported the election loser (4.6 percent lower for males and 5.3 lower for females).

Richard A. Dunn, Ph.D., lead author of the study, credits the power of social cohesion, “Sure, supporting the loser stinks, but if everyone around you supported the loser, it isn’t as bad because you feel connected to those around you. In other words, it is more comforting to be a Democrat in Massachusetts or Rhode Island when George W. Bush was re-elected than to be the lonely Democrat in Idaho or Oklahoma.”

The authors propose that people gain a sense of community in having voted for the losing candidate, and that keeps them from killing themselves. People in “swing” states are presumably out of luck either way.

XMRV, CFS, and the Nature of Science

On the last episode of TWiV, we talked about XMRV, a retrovirus that appears to infect some people. A couple of studies have found correlations between XMRV infection and diseases, including chronic fatigue syndrome (CFS) and prostate cancer. A couple of other studies have tried to reproduce those results, and failed. After the episode, we got a lot of comments on the TWiV blog and on alandove.com from CFS patients, some of them quite vehement (prostate cancer patients didn’t get nearly as riled up).

What really seemed to set people off was my statement that we don’t know what causes CFS – a position I considered pretty uncontroversial. I elaborated on the show, pointing out that there is evidence both for and against infectious, environmental, and psychiatric causes for this disease, and that it could very well be some combination of those. Apparently, using the word “psychiatric” in this context, even with all of those caveats, was tantamount to dropping a match into a can of gasoline.

I made a few attempts at clarification in the blog comments, but it soon became apparent that the CFS patients and I were arguing from entirely different premises, and could never agree. They’re ill – often debilitatingly so – and want clear answers and a cure immediately, if not sooner. I’m not ill (thankfully), and I think like a scientist. And that’s the real problem.

Science has two great strengths, and two great weaknesses. Its strengths are that it is excruciatingly thorough, and its conclusions are as close as humans are capable of getting to objective Truth. Those are also its weaknesses.

The price of thoroughness is time. Scientists do not leap to conclusions, we crawl to them. It takes us years to determine the simplest things: that DNA is the genetic material, that poliovirus causes acute flaccid paralysis, that sunspot numbers rise and fall in a predictable cycle. Even then, we swaddle our answers in layers of “mostly,” “sometimes,” and “probably.” Proteins and RNA can transmit some genetic information, poliovirus infection can be asymptomatic, and some sunspot cycles are longer than others.

People who are suffering don’t want probabilities and uncertanties. They want answers. When they hear one that sounds good, they’ll grab it and go before anyone can say “but…” Say that you found XMRV in 60% of CFS patients and only 4% of controls in one small study, and some patients will hear “XMRV causes CFS, case closed, now let’s start taking antivirals.” Try to remind them that the science isn’t anywhere near done, that in fact it’s barely started, and you’re now threatening their established view of the world.

The second feature of science is its unique claim to truth. Its conclusions are equally valid for Christians, Muslims, Jews, and atheists. They’re true even if every neuron in your brain denies them. A postmodernist can scream until he’s blue in the face that the Newtonian frame of reference is just one of many equally legitimate world views, and that non-Newtonian claims to reality have just as much validity. Nonetheless, if he steps off a tenth-floor balcony, he will accelerate downward at 9.8 meters per second per second (minus air resistance). It works every time.

Sometimes telling the truth, or even listing all of the things that might be true, is bad diplomacy. “Well, Honey, it could be the dress, or it could be that your hips actually are big.” The statement certainly presents two possible truths, but the listener isn’t likely to hear them dispassionately. Similarly, saying that CFS could have infectious, environmental, and/or psychiatric causes presents a list of possible truths. The current science has not ruled out any of those possibilities, which aren’t even mutually exclusive.

Unfortunately, the word “psychiatric” carries heavy freight. Our society stigmatizes mental illness, and the current treatments for most psychiatric conditions range from mediocre to nonexistent. Saying that a disease could be psychiatric is saying that it could be ostracizing and incurable. That’s not something a CFS patient wants to hear. Many of them probably stopped reading after the previous paragraph.

I can’t stop thinking like a scientist, and won’t stop speaking and writing like one. What I will try to stop doing is arguing data against people whose objections rest on emotion. You’re entitled to your beliefs. Just try not to step off any balconies.

How Many Reps?

There’s a longstanding debate in gyms around the world: is it better to do many repetitions (reps) of relatively low weights, or a few repetitions of relatively high weights? Different players in the fitness industry spend huge sums of money promoting one strategy or the other, and gym rats spend even more to follow the plan they believe in. Personally, I’ve been on the fence about it for years, and tend to switch between one regimen and the other every few months. Now a new study from McMaster University in Canada claims to have resolved the issue. As the authors explain in an accompanying press release:

“Rather than grunting and straining to lift heavy weights, you can grab something much lighter but you have to lift it until you can’t lift it anymore,” says Stuart Phillips, associate professor of kinesiology at McMaster University.

The study used light weights that represented a percentage of what the subjects could lift. The heavier weights were set to 90% of a person’s best lift and the light weights at a mere 30% of what people could lift. “It’s a very light weight,” says Phillips noting that the 90-80% range is usually something people can lift from 5-10 times before fatigue sets in. At 30%, Burd reported that subjects could lift that weight at least 24 times before they felt fatigue.

Barbell weights. Image courtesy Flickr user dno1967.

Barbell weights. Image courtesy Flickr user dno1967.

Phillips and his colleagues conclude that as long as one lifts to exhaustion, the lighter weight/higher rep workout is better at building muscle mass. There are, of course, some major caveats. Like virtually every exercise physiology study ever done, this one used a sample of about a dozen college students. Such a tiny, nonrepresentative group hardly settles the debate for the general population. In addition, the study didn’t really look at muscle mass, only a short-term test of a set of biomarkers that are believed to correlate with muscle building.

Nonetheless, it was nice to see this right after my morning workout – which today consisted mostly of triple sets of eight reps (24 reps total) for each lift. Now if you’ll excuse me, I have to treat myself to a good high-protein lunch.

Genetically Engineered Canola Escapes

I bet a poster being presented today at the Ecological Society of America annual meeting is going to set off a loud discussion:

Scientists currently performing field research in North Dakota have discovered the first evidence of established populations of genetically modified plants in the wild. Meredith G. Schafer from the University of Arkansas and colleagues from North Dakota State University, California State University, Fresno and the U.S. Environmental Protection Agency established transects of land along 5,400 km of interstate, state and county roads in North Dakota from which they collected, photographed and tested 406 canola plants.

The results—which were recorded in early July and are set to be presented at ESA’s Annual Meeting in Pittsburgh—provide strong evidence that transgenic plants have established populations outside of agricultural fields in the U.S. Of the 406 plants collected, 347 (86%) tested positive for CP4 EPSPS protein (confers tolerance to glyphosate herbicide) or PAT protein (confers tolerance to glufosinate herbicide).

That’s not terribly surprising, as environmentalists have so far prevented seed companies from including genes that would have prevented these crops from spontaneously re-seeding. What’s more, the escaped plants appear to be interbreeding:

“There were also two instances of multiple transgenes in single individuals,” said one of the study’s coauthors Cynthia Sagers, University of Arkansas. “Varieties with multiple transgenic traits have not yet been released commercially, so this finding suggests that feral populations are reproducing and have become established outside of cultivation. These observations have important implications for the ecology and management of native and weedy species, as well as for the management of biotech products in the U.S.”

Let the screaming begin.

(Via Eurekalert).

The Surpsingly Complicated Problem of “Dolphin-Safe” Tuna

There’s a fascinating post about “dolphin safe” tuna at Southern Fried Science today. It starts off like this:

The commonly believed narrative about dolphin-safe tuna goes something like this: Lots of dolphins were being killed by tuna fishermen, outraged environmentalists led a massive PR campaign, legions of adorable children wrote to their elected officials, elected officials changed the rules to protect dolphins, and everything is better now. Hooray, we saved an innocent species and helped the environment!

That narrative is a great story. It shows that if a few people who care can convince others that their cause is just, there’s no limit to what we can accomplish. It’s inspiring. Too bad it’s not really true. As it turns out, we made things worse- a LOT worse.

The only time I eat tuna is when it’s served on a sushi platter – I find it cooks up too dry, and the canned stuff reminds me too much of cat food. Nonetheless, I was fascinated by the nuances of this fishery. Of course, I was also disappointed by the apparent attitude of the environmental campaigners who got this disastrous policy change enacted. Read the full post and make up your own mind.